Palign

The ProteinALIGNment (Palign) programs are a set of programs for sequence searches. They can perform standard dynamic programming, heuristic fasta like searches and profile-profile alignments. Unfortunately the package is not very well documented, but is all available for free under a GPL like license. Palign can be used for many type of alignment problems, it is certainly not always the fastest of all programs but it is very flexible and can:

1. Align two sequences and search a database with a sequence
2. Align a sequence and a profile
3. Include and combine secondary structure information into the alignments
4. Read sequences, profiles etc in many formats
5. Perform profile-profile searches/alignments using different algorithms

Some Papers where Palign has been used

1. Tomas Ohlson and Arne Elofsson "Profnet, a method to derive profile--profile alignment scoring functions that improves the alignments of distantly related proteins.", BMC Bioinformatics 2005 6:253 pdf
2. Tomas Ohlson, Björn Wallner and Arne Elofsson "Profile--profile methods provide improved fold--recognition. A study of different profile-profile alignment methods.", Proteins 2004 57(1):188-97. pdf
3. "Using evolutionary information for the query and target improves fold recognition." Björn Wallner, Huisheng Fang, Tomas Ohlson, Johannes Frey-Skött and Arne Elofsson, 2004 Proteins 54(2):342-350 pdf
4. A study on how to best align protein sequences. Arne Elofsson 2002 Proteins: Struct. Funct. Genet. 46(3):300-309 pdf
5. ``Improved detection of homologous membrane proteins by inclusion of information from topology predictions,'' Maria Hedman, Hans De Loof, Gunnar von Heijne and Arne Elofsson2002 Protein Science11(3):652-658 pdf
6. ``Identification of related proteins, a comparative study of sequence and threading methods.'' Erik Lindahl and Arne Elofsson, 2000 J. Mol. Biol. 295:613-625 pdf

Some relevant links

1. palign.tar.gz Source Code and Linux binaries
2. instructions on how to install, use and compile.